Expanded genetic variation (SNP) and phenomics (image based) dataset for Populus trichocarpa

Nagle, Michael F; Yuan, Jialin; Kaur, Damanpreet; Ma, Cathleen; Peremyslova, Ekaterina; Jiang, Yuan; Nino de Rivera, Alexo; Jowdy, Sara; Chen, Jin-Gui; Feng, Kai; Yates, Timothy; Yates, Timothy B; Tuskan, Gerald A; Muchero, Wellington; Li, Fuxin; Strauss, Steven H

doi:10.25983/2263365

DOE OSTI · 2263365

Expanded genetic variation (SNP) and phenomics (image based) dataset for Populus trichocarpa

Nagle, Michael F·Yuan, Jialin·Kaur, Damanpreet·Ma, Cathleen·Peremyslova, Ekaterina·Jiang, Yuan·Nino de Rivera, Alexo·Jowdy, Sara·Chen, Jin-Gui·Feng, Kai·Yates, Timothy·Yates, Timothy B·Tuskan, Gerald A·Muchero, Wellington·Li, Fuxin·Strauss, Steven H

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Abstract

The image dataset consists of 11,791 images representing 1,219 genotypes of Populus trichocarpa undergoing in planta regeneration. Genotypes were imaged with a median of four weekly timepoints and a median of two replicates each. A representative and diverse subset of 249 images was annotated using the IDEAS annotation interface (ideas.eecs.oregonstate.edu) and these annotated images were used to train a deep semantic segmentation model (PSPNet), which was deployed for inference over the entire dataset. Annotated classes include specific stages of regeneration (callus and shoot) in addition to unregenerated plant material and background. Statistics of relative tissue area were extracted and used for downstream genetic association mapping in a genome-wide association study. The SNP dataset consists of over 40 million single-nucleotide polymorphisms across 1,323 wild accessions of Populus trichocarpa

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09 BIOMASS FUELS Populus Trichocarpa, GWAS, phenotyping

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Nagle, Michael F, Yuan, Jialin, Kaur, Damanpreet, Ma, Cathleen, Peremyslova, Ekaterina, Jiang, Yuan, Nino de Rivera, Alexo, Jowdy, Sara, Chen, Jin-Gui, Feng, Kai, Yates, Timothy, Yates, Timothy B, Tuskan, Gerald A, Muchero, Wellington, Li, Fuxin, Strauss, Steven H. 2023-12-27. Expanded genetic variation (SNP) and phenomics (image based) dataset for Populus trichocarpa. https://doi.org/10.25983/2263365

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